Hi,
The data i hav is something like this, x is a list
x[0] = ['1','2345','96','2456','3','3456','94','3478']
x[1] = ['3','3456','94','3478',1','4345','96','4456']
x[-1] = ['4','223','91','445']
similarly upto 24 elements in list x. (no of elements in x[0] to x[-1] are not same)
I need to write a loop to take out alternate values in all the list, like for x[0] ['1','96'] ['2345'2456'] ['3','94'] and ['3456','3478']and store in different variables . Similatly the loop should return alternate values for all from x[0] to x[-1].
Someone please help me...
You should probably look into some sort of structured data (i.e., using numpy), as doing manipulations on lists like this is fairly expensive. That said, this works:
N.B.: apparently code formatting gets stripped, so you'll have to add in appropriate indentation yourself.
In [1]: x = []
In [2]: x.append(['1','2345','96','2456','3','3456','94','3478'])
In [4]: x.append(['3','3456','94','3478','1','4345','96','4456'])
In [5]: x.append(['4','223','91','445'])
In [6]: x[0]
Out[6]: ['1', '2345', '96', '2456', '3', '3456', '94', '3478']
In [7]: x[1]
Out[7]: ['3', '3456', '94', '3478', '1', '4345', '96', '4456']
In [8]: x[-1]
Out[8]: ['4', '223', '91', '445']
In [27]: def split_list(l):
....: r1 = range(0, len(l), 2)
....: r2 = range(1, len(l), 2)
....: output = []
....: for i in range(len(r1)/2):
....: output.append((l[r1[i*2]], l[r1[i*2+1]]))
....: output.append((l[r2[i*2]], l[r2[i*2+1]]))
....: return output
In [30]: for item in x:
....: print split_list(item)
....:
[('1', '96'), ('2345', '2456'), ('3', '94'), ('3456', '3478')]
[('3', '94'), ('3456', '3478'), ('1', '96'), ('4345', '4456')]
[('4', '91'), ('223', '445')]
For a single list, you can get alternate elements using list comprehensions:
>>>x=[1,2,3,4,5]
>>>[x[i] for i in range(0,len(x),2)]
[1, 3, 5]
go from there to apply to your case.
Thank you very much Brett Olsen . I would be really great full if you could do me another help. Is it possible to append all values into a new list like a = [1,96] b = [2345,2456] because there is a need of addition and subtraction with these values for me to extract sequence from genome sequences. After defining function, i wrote:
for item in x:
a = split_list(item)
and tried to print a[0],,,, but it didnt work.
It's not very clear to me what you're looking for. Could you tell me what this data is and what you're trying to do with it? I think if I have a little more information it would be easier for me to help you do what you need to do.
My work is on identification and characterization of microrna. The list x=[] is the parsed result of stand alone blast using biopython. the values in x is accordingly (query start,query end,subjct start,subject end,) of the alignment. I need to extract query sequence from the fasta file.
eg: total length of mirna(subject) = 96
in alignment, subject start = 3 ; subject end = 94 (2 nucleotides 1,2 in mirna are not included in alignment at start and similarly 95,96 not included in the end.)
if query start is from 2345 to query end 2456. I need to extract query from (2345-2) to (2456+2) ie; making the query equal to the length of microrna.
I am very confused with this and making it complicated. Hope you could help me.
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology